Multimodal Ligand Research Articles

Effect of Monovalent Cations on the Structure and Dynamics of Multimodal Chromatographic Surfaces.

While multimodal (MM) chromatography is a promising approach for purifying proteins, the lack of a fundamental understanding of how ion-ligand interactions govern selectivity limits its use in the biopharmaceutical industry. This study uses molecular dynamics simulations to study the interactions between simple monovalent cations and two commonly used structurally similar multimodal chromatography ligands, the Capto ligand and Nuvia cPrime, immobilized on the surface. On the Capto ligand surface, ion presence and type play a key role in modulating the formation of phenyl rings and carboxylate clusters. The flexible linkage attaching the Capto ligand to the self-assembled monolayer (SAM) surface allowed multiple ligands to form interactions with the small cations, while large cations interacted less strongly, following the order Li+ > Na+ > K+ > Cs+. Thus, smaller cations resulted in greater ordering on the surface and lower ion diffusivities, while larger cations resulted in less ordering and higher ion diffusivities, following the order Li+ < Na+ < K+ < Cs+. In contrast, due to the rigid attachment of Nuvia cPrime to the SAM surfaces, the cations bound less strongly and had a much smaller effect on ligand clustering or ordering. Additionally, ions in the presence of the Nuvia cPrime surface had generally greater diffusivities than those in the presence of the Capto ligand. Overall, the interaction of cations with the multimodal ligands can lead to unique configurations on the SAM that likely contribute to differential behavior in biological separations.

Purification of a monoclonal antibody using a novel high-capacity multimodal cation exchange nonwoven membrane

A high-capacity, multimodal cation exchange (MMC) chromatographic membrane was developed by conjugating a multimodal ligand – 2-mercaptopyridine-3-carboxylic acid (MPCA) – on a polybutylene terepthalate (PBT) nonwoven fabric. The membrane features an equilibrium binding capacity of ≈ 1000 mg of human polyclonal IgG (IgG) per g of membrane and dynamic binding capacities (DBC10%) ranging from 77.5 to 115.1 mg/mL (residence times of 1 and 5 min, respectively); these values are 2-to-3-fold higher than those of commercial MMC adsorbents. The effects of buffer composition, pH, conductivity on the binding behavior of the MMC-MPCA membrane were investigated in detail. As a moderate cation exchange binder, MPCA enables effective protein elution using buffers with mild pH (8.0–9.0) and conductivity (≈13 mS/cm), thus circumventing the harsh conditions often needed in multimodal chromatography. The MMC-MPCA membrane was evaluated for product capture in bind-and-elute mode on a Chinese hamster ovary (CHO) cell culture harvest containing therapeutic monoclonal antibodies, using commercial multimodal (Capto MMC and MX-Trp-650M) and affinity (AF-rProtein A HC-650F) resins as controls. The MMC-MPCA membrane outperformed the multimodal resins in terms of binding capacity as well as clearance of host cell proteins (HCPs) and aggregates. The membrane was then evaluated by polishing the mAb from a Protein A eluate in bind-and-elute mode. The MMC-MPCA membrane reduced the level of high molecular weight components from 11% to 4% and the HCP content from 1319.7 ppm to 48.7 ppm (LRV of 1.4). Most notably, proteomics analysis of the product demonstrated the clearance of a significant fraction of persistent, high-risk HCPs from the Protein A eluate.

CIM monolithic chromatography as a useful tool for endotoxin reduction and purification of bacteriophage particles supported with PAT analytics

Bacteriophages represent immense potential as therapeutic agents. Many of the most compelling applications of bacteriophages involve human therapy, some pertinent to gene therapy, others involving antibiotic replacement. Phages themselves are considered safe for humans. However, phage lysates may contain many kinds of harmful by-products, especially endotoxins of gram-negative bacteria and protein toxins produced by many pathogenic bacterial species. In bacteriophage research and therapy, most applications ask for highly purified phage suspensions, as such it is crucial to reduce proteins, endotoxins, DNA and other contaminants.In this article we present an efficient two-step chromatographic purification method for P. aeruginosa bacteriophage PP-01, using Convective Interaction Media (CIM®) monoliths, that is cGMP compliant and easy to scale-up for most stringent production of the therapeutic phage. First chromatographic step on CIMmultus OH resulted in 100% bacteriophage recovery with a reduction of 98 % protein and more than 99 % DNA content. Polishing was conducted using three different column options, CIMmultus with QA, H-Bond and PrimaS ligands. For PP-01 bacteriophage all three different options worked, but multimodal ligands H-Bond and PrimaS outperformed traditional QA in endotoxin removal (7 log step reduction). Additionally, an HPLC analytical method was developed to estimate phage concentration and impurity profile in different in-process samples. The HPLC method shows good correlation with drop assay titration, provides useful insights and can be run very fast with just 20 min per sample analysis.

Microfluidics as a high-throughput solution for chromatographic process development – The complexity of multimodal chromatography used as a proof of concept

High-throughput technologies are fundamental to expedite the implementation of novel purification platforms. The possibility of performing process development within short periods of time while saving consumables and biological material are prime features for any high-throughput screening device. In this work, a microfluidic device is evaluated as high-throughput solution for a complete study of chromatographic operation conditions on ten different multimodal resins. The potential of this class of purification solutions is generally hindered by its complexity. Taking this into consideration, the microfluidic platform was herein applied and assessed as a tool for high-throughput applications. The commercially available multimodal ligands were studied for the binding of three antibody-based biomolecules (polyclonal mixture of whole antibodies, Fab and Fc fragments) at different pH and salt conditions, in a total of 450 experiments. The results obtained with the microfluidic device were comparable to a standard 96-well filtering microplate high-throughput tool. Additionally, five of the ten multimodal ligands tested were packed into a bench-scale column to perform a final validation of the microfluidic results obtained. All the data acquired in this work using different screening protocols corroborate each other, showing that microfluidic chromatography is a valuable tool for the fast implementation of a new purification step, particularly, if the goal is to narrow the downstream possibilities by being a first point of decision.

Elaboration of multimodal ligands based on BOX units: Toward full zinc release in Zn(II) complexes by external stimulation

The development of molecular switches such as photochromic and electrochromic systems still represents a major concern in numerous application fields. If numerous pure organic switch families have been explored so far, concerning the coordination compounds, the choice seems more limited. In this context, we are exploring the possibility to elaborate a new addressable ligand family based on benzazolo-oxazolidine (BOX) moiety, a poorly investigated switch family, known for its acido-, electro- and photochromism properties. As proof of concept, two ligands bearing a BOX moiety were prepared using a pyridine as metal binding site after what corresponding Zn(II) complexes were synthesized and characterized. The acido-, electro- and photochemical behaviors of the free ligand as well as complexes were studied. This study reveals a subtle and interesting tautomeric equilibrium between oxazolidine ring opening and pyridine protonation whatever the nature of the stimulation. More interestingly, it conducts to observe the possibility to catch and release zinc ion on demand by using two external and orthogonal stimulations.

Precise control of immune modulation using DNA scaffold-mediated biomaterial functionalization

Abstract Synthetic materials displaying multi-modal ligands with exact chemiophysical properties for immune modulation are valuable research tools and a promising therapeutic platform. However, precise chemical conjugation of multiple proteins on biomaterial surfaces is challenging. Through DNA hybridization-mediated biomolecule loading, we achieved high density and precise ratiometric control of multiple ligands on nano-/micro-particles. We found increasing ratios of anti-CD3 to anti-CD28, 1:5, 1:3, 1:1, 3:1 to 5:1, on microparticles yielded a linear increase of ex vivo expansion of primary human CD4+ and CD8+ T cells until reaching a plateau at 3:1 ratio. For CD8+ T cells, the ratio of 3:1 resulted in the highest percentage of central memory cells, 51.4 ± 7.2% vs. 14.4 ± 7.6% for 1:5 ratio (n = 5 donors). Particle surface presentation of IL-2 using an anti-IL-2 antibody (in trans to CD3/28 particles) yielded ~3 fold more ex vivo expansion of CD4+ and CD8+ T cells in 14 days when compared to the equivalent dose of soluble IL-2. Using intratumoral injection of microparticles presenting a ligand for a synthetic Notch receptor, we locally induced chimeric antigen receptor (CAR) expression on systemically infused engineered T cells and observed CAR T cell killing of the injected tumors, while sparing the uninjected identical tumors in the contralateral flank. These results highlight the potential of this platform in achieving better control of therapeutic cell manufacture and local tuning of immunotherapies. Ongoing work is using DNA origami-mediated patterning to dissect spatial requirements of various T cell activating ligands to better understand critical parameters of T cell activation with the goal to improve the design of immunotherapies.

Data-driven molecular design for discovery and synthesis of novel ligands: a case study on SARS-CoV-2

Bridging systems biology and drug design, we propose a deep learning framework for de novo discovery of molecules tailored to bind with given protein targets. Our methodology is exemplified by the task of designing antiviral candidates to target SARS-CoV-2 related proteins. Crucially, our framework does not require fine-tuning for specific proteins but is demonstrated to generalize in proposing ligands with high predicted binding affinities against unseen targets. Coupling our framework with the automatic retrosynthesis prediction of IBM RXN for Chemistry, we demonstrate the feasibility of swift chemical synthesis of molecules with potential antiviral properties that were designed against a specific protein target. In particular, we synthesize an antiviral candidate designed against the host protein angiotensin converting enzyme 2 (ACE2); a surface receptor on human respiratory epithelial cells that facilitates SARS-CoV-2 cell entry through its spike glycoprotein.This is achieved as follows. First, we train a multimodal ligand–protein binding affinity model on predicting affinities of bioactive compounds to target proteins and couple this model with pharmacological toxicity predictors. Exploiting this multi-objective as a reward function of a conditional molecular generator that consists of two variational autoencoders (VAE), our framework steers the generation toward regions of the chemical space with high-reward molecules. Specifically, we explore a challenging setting of generating ligands against unseen protein targets by performing a leave-one-out-cross-validation on 41 SARS-CoV-2-related target proteins. Using deep reinforcement learning, it is demonstrated that in 35 out of 41 cases, the generation is biased towards sampling binding ligands, with an average increase of 83% comparing to an unbiased VAE. The generated molecules exhibit favorable properties in terms of target binding affinity, selectivity and drug-likeness. We use molecular retrosynthetic models to provide a synthetic accessibility assessment of the best generated hit molecules. Finally, with this end-to-end framework, we synthesize 3-Bromobenzylamine, a potential inhibitor of the host ACE2 protein, solely based on the recommendations of a molecular retrosynthesis model and a synthesis protocol prediction model. We hope that our framework can contribute towards swift discovery of de novo molecules with desired pharmacological properties.

Identification of preferred multimodal ligand-binding regions on IgG1 FC using nuclear magnetic resonance and molecular dynamics simulations.

In this study, the binding of multimodal chromatographic ligands to the IgG1 FC domain were studied using nuclear magnetic resonance and molecular dynamics simulations. Nuclear magnetic resonance experiments carried out with chromatographic ligands and a perdeuterated 15 N-labeled FC domain indicated that while single-mode ion exchange ligands interacted very weakly throughout the FC surface, multimodal ligands containing negatively charged and aromatic moieties interacted with specific clusters of residues with relatively high affinity, forming distinct binding regions on the FC . The multimodal ligand-binding sites on the FC were concentrated in the hinge region and near the interface of the CH 2 and CH 3 domains. Furthermore, the multimodal binding sites were primarily composed of positively charged, polar, and aliphatic residues in these regions, with histidine residues exhibiting some of the strongest binding affinities with the multimodal ligand. Interestingly, comparison of protein surface property data with ligand interaction sites indicated that the patch analysis on FC corroborated molecular-level binding information obtained from the nuclear magnetic resonance experiments. Finally, molecular dynamics simulation results were shown to be qualitatively consistent with the nuclear magnetic resonance results and to provide further insights into the binding mechanisms. An important contribution to multimodal ligand-FC binding in these preferred regions was shown to be electrostatic interactions and π-π stacking of surface-exposed histidines with the ligands. This combined biophysical and simulation approach has provided a deeper molecular-level understanding of multimodal ligand-FC interactions and sets the stage for future analyses of even more complex biotherapeutics.

Synthesis and characterization of chitosan mini-spheres with immobilized dye as affinity ligand for the purification of lactoperoxidase and lactoferrin from dairy whey

Lactoperoxidase (LP) and lactoferrin (LF) are two interesting proteins present in dairy whey due to their antioxidant, anti-inflammatory, antibacterial, antiviral and antifungal properties. LP and LF are traditionally purified using cation-exchange chromatography, but since the concentration of these proteins in sweet whey are very low (0.03–0.06 g/L for LP and around 0.08–0.20 g/L for LF), clarification, diafiltration, concentration and/or depletion of others whey proteins prior to the ion-exchange chromatography is needed to obtain good adsorption yields. After their elution from the matrix, the overall process results in variable yields. Due to their similar physico-chemical properties, a high cross-contamination is usually present, especially for the LP fraction, where part of the LF is co-eluted.The development of novel supports with immobilized affinity and/or multimodal ligands aims to the direct adsorption of the target proteins even at low concentration and without the need of a pre-treatment of the source. Herein, a new, low-cost support material using chitosan mini-spheres with Orange R-HE triazine dye as immobilized ligand (CMS-Orange R-HE) was synthesized, physico-mechanically characterized and used for the purification of LP and LF by a one-step direct adsorption from dairy whey and a two-step elution process, with minor cross-contamination. CMS-Orange R-HE matrix showed a compression modulus of 47.6 ± 9.8 kPa, predominantly elastic deformation and an open-porous structure with mesopores around 5–20 nm and without ink-bottle pores, ideal for protein purification applications. The affinity between LP and LF for CMS-Orange R-HE matrix was characterized using the Langmuir isotherm model (Kd = 0.48 ± 0.07 mg/mL and 0.31 ± 0.09 mg/mL; qmax = 77.5 ± 4.0 mg/g and 56.0 ± 2.1 mg/g, respectively). Adsorption studies showed that LP interaction with CMS-Orange R-HE was partially influenced by the presence of ionic strength (p < 0.05), whereas LF adsorption was not. These differences of both electrostatic and hydrophobic interactions between LP and LF with the CMS-Orange R-HE matrix were used to develop a differential elution process using Response Surface Methodology (RSM). By one-step direct adsorption from dairy whey and two differential elution steps –by using the CMS-Orange R-HE matrix- LP and LF were obtained with good yields (≈70% for LP and ≈60% for LF), high purity and with minor cross-contamination between them. The strategy presented here, could be applied in other cases of cross-contamination between two proteins, being especially interesting for its application in multimodal chromatography.

Improved ionic-liquid-functionalized macroporous supports able to purify nucleic acids in one step.

Nucleic acids are relevant biopolymers in therapy and diagnosis, for which their purity and biological activity are of crucial relevance. However, these features are difficult to achieve by cost-effective methods. Herein, we report the functionalization of a macroporous chromatographic support functionalized with an ionic liquid (IL) with remarkable performance to purify nucleic acids. An initial screening with distinct IL chemical structures supported in silica was carried out, allowing to identify the IL 1-methyl-3-propylimidazolium chloride as the most promising ligand. A chromatographic macroporous matrix able to be used in preparative liquid chromatography was then functionalized and binding/elution studies were performed. The IL 1-methyl-3-propylimidazolium chloride acts as a multimodal ligand with a remarkable dynamic binding capacity. This macroporous support allows the (one-step) purification of nucleic acids, namely small RNAs, ribosomal RNA, and genomic DNA, from a bacterial lysate, and can be regenerated and reused without compromising its separation performance.

The Role of Ligand-Ligand Interactions in Multimodal Ligand Conformational Equilibria and Surface Pattern Formation.

Multimodal chromatography uses multiple modes of interaction such as charge, hydrophobic, or hydrogen bonding to separate proteins. Recently, we used molecular dynamics (MD) simulations to show that ligands immobilized on surfaces can interact and associate with neighboring ligands to form hydrophobic and charge patches, which may have important implications for the nature of protein-surface interactions. Here, we study interfacial systems of increasing complexity-from a single immobilized multimodal ligand to high density surfaces-to better understand how ligand behavior is affected by the presence of a surface and the presence of other ligands in the vicinity, and how this behavior scales to larger systems. We find that tethering a ligand to a surface restricts its conformations to a subset of those observed in free solution, yet the ligand maintains flexibility in the plane of the surface and can form contacts with neighboring ligands. We find that although the formation of a contact between two neighboring ligands is slightly unfavorable, three neighboring ligands exhibit a preference for the formation of a fully connected cluster. To explore how these trends in ligand association extend to a larger surface with high density of ligands, we performed coarse-grained Monte Carlo (MC) simulations of a 132-ligand surface using ligand interactions parametrized based on free energies obtained from the three-ligand MD simulations. Despite their simplicity, the coarse-grained simulations qualitatively capture the cluster size distribution of ligands observed in detailed MD simulations. Quantitative differences between the two suggest opportunities for improvements in the coarse-grained energy function for efficient predictions of cluster and pattern formations. Our approach presents a promising route to the engineering of multimodal patterns for future chromatographic resin design.

Optimizing the Performance of Chromatographic Separations Using Microfluidics: Multiplexed and Quantitative Screening of Ligands and Target Molecules

The optimization of chromatography ligands for the purification of biopharmaceuticals is highly demanded tomeet the needs of the pharmaceutical industry. In the case of monoclonal antibodies (mAbs), synthetic ligands comprising multiple types of interactions (multimodal) provide process and economic advantages compared to protein-based affinity ligands. However, optimizing the operation window of these ligands requires the development of effective high-throughput screening platforms. Here, a novel microfluidics-based methodology to perform rapid and multiplexed screening of various multimodal ligands relative to their ability to bind different target molecules is demonstrated. The microfluidic structure comprises three individual chambers (≈8 nL each) packed with different types of chromatography beads in series with the feed flow. An artificial mixture composed of immunoglobulin G (IgG) and bovine serum albumin, labeled with different thiol-reactive neutral fluorescent dyes, is used as a model to quantitatively optimize the performance (yield and purity) of the separation. This approach can potentially be used as a predictive analytical tool in the context of mAb purification, allowing low consumption of molecules and providing results in <3 min. Furthermore, this versatile approach can potentially be extended not only with respect to the number of different resins and target molecules, but also for parallel analysis of multiple conditions.

Conformational Equilibria of Multimodal Chromatography Ligands in Water and Bound to Protein Surfaces.

Multimodal chromatography uses small ligands with multiple modes of interaction, e.g., charged, hydrophobic or hydrogen bonding, to separate proteins from complex mixtures. The mechanism by which multimodal ligands interact with proteins is expected to be affected by ligand conformations, among other factors. Here, we study conformational equilibria of two commercially used multimodal cation exchange ligands, Capto MMC and Nuvia cPrime, in a range of solvents, a Lennard-Jones (LJ) liquid, ethanol, and water, using molecular dynamics (MD) simulations. By mapping ligand conformations onto two key torsion angles, ω and φ, in these solvents and in low and high dielectric media, we quantify the relative importance of intramolecular and solvent-mediated interactions. In a high dielectric medium, Capto MMC preferentially samples three conformations, which are stabilized by a combination of an intramolecular torsion potential (on ω) and LJ interactions. In an LJ liquid, solvent molecules compete with intramolecular interactions while simultaneously providing an osmotic force, stabilizing both closer and farther distances between ligand sites. This has the overall effect of "flattening out" the conformational landscape. Interestingly, in ethanol and water, hydrogen bonding between the amide hydrogen and solvent molecules stabilizes two additional conformations of Capto MMC in which ω takes on less favorable cis-like configurations. MD simulations of ligands in free solution with three therapeutic antibody fragments show that ligand conformational equilibria remain effectively unchanged upon binding to proteins. Although, there is 20-30% dehydration of the overall ligand upon binding, the hydrogen-bonding sites are dehydrated to a much smaller extent, particularly in cis-like configurations. Conformational preferences of Nuvia cPrime are similar to that of Capto MMC, except for the effect of symmetry arising from the absence of an alkyl thiol tail. Characterizing the conformational equilibria of these two ligands in free solution and bound to a protein provides a foundation for developing a mechanistic understanding of protein-multimodal ligand interactions.

Nuclear Magnetic Resonance at the Interface: Identifying Preferred Binding Regions in Multimodal Cation Exchange Chromatography using Functionalized Nanoparticles

The Fc domain is an important component of complex molecules such as monoclonal antibodies (mAb) based biologics as well as fusion proteins and is highly conserved across a given class of mAbs. Recent work in our lab has shown the importance of specific domains towards binding for mAbs to multimodal (MM) cation exchange chromatographic systems. In this collaborative work, we employ a combination of Nuclear Magnetic Resonance (NMR) spectroscopy and Umbrella sampling simulations to develop a fundamental understanding of how multimodal ligands and surfaces interact with the Fc domain. We performed NMR titration experiments with isotopically labeled Fc and ∼15 nm diameter gold nanoparticles (Au NPs) functionalized with Self Assembled Monolayers (SAMs) presenting different MM ligands at different ligand densities. The results showed the interface of CH2 and CH3 domains and the hinge region to be preferred binding regions for interaction of Fc to MM ligand surfaces. These flexible regions on the protein surface which are rich in positive and aliphatic residues are important for the binding of Fc to MM ligand surfaces. Further, to shed light on the binding mechanisms, we performed umbrella sampling with the Fc held at key orientations above a SAM surface presenting MM ligands at relevant ligand densities similar to those tested experimentally. These simulations suggested that as the Fc was brought close to the surface, the residues near the hinge region first made contact with the surface followed by a tighter binding facilitated by interaction of His, Val, Leu and Ile residues at the interface of the CH2 and CH3 domains. This combined experimental and simulations approach enabled us to develop a molecular level understanding of the binding for complex biological products in MM CEX systems.

Multimodal Ligand Binding Studies of Human and Mouse G-Coupled Taste Receptors to Correlate Their Species-Specific Sweetness Tasting Properties.

Taste signaling is a complex process that is linked to obesity and its associated metabolic syndromes. The sweet taste is mediated through a heterodimeric G protein coupled receptor (GPCR) in a species-specific manner and at multi-tissue specific levels. The sweet receptor recognizes a large number of ligands with structural and functional diversities to modulate different amplitudes of downstream signaling pathway(s). The human sweet-taste receptor has been extremely difficult to study by biophysical methods due to the difficulty in producing large homogeneous quantities of the taste-receptor protein and the lack of reliable in vitro assays to precisely measure productive ligand binding modes that lead to activation of the receptor protein. We report here a multimodal high throughput assay to monitor ligand binding, receptor stability and conformational changes to model the molecular ligand-receptor interactions. We applied saturation transfer difference nuclear magnetic resonance spectroscopy (STD-NMR) complemented by differential scanning calorimetry (DSC), circular dichroism (CD) spectroscopy, and intrinsic fluorescence spectroscopy (IF) to characterize binding interactions. Our method using complementary NMR and biophysical analysis is advantageous to study the mechanism of ligand binding and signaling processes in other GPCRs.

Investigating the impact of aromatic ring substitutions on selectivity for a multimodal anion exchange prototype library

The increasing prevalence of low pI non-mAb therapeutics as well as current challenges in mAb-aggregate separations and low recoveries motivate further development in the multimodal anion exchange (MM AEX) space. In this work, linear salt gradient experiments at pH 7 were used to evaluate the retention of model proteins (with pI from 3.4 to 6.8) in 17 novel MM AEX prototype systems. The ligands were organized into three series. Series 1 extended previous work in multimodal ligand design and included a hydroxyl variant and linker length variants. Series 2 and 3 investigated the nature of hydrophobicity in MM AEX systems by adding hydrophobic (series 2) or fluorine (series 3) substituents to a solvent exposed phenyl ring. Compared to the commercial resin Capto Adhere, the series 1 and 3 ligands exhibited weaker binding, while some of the series 2 aliphatic prototypes showed dramatically increased retention and unique selectivities. Within series 1, the model proteins eluted earlier in the gradient as the charge-hydrophobic group distance on the ligand was increased from 4.9 Å to 8.5 Å. For the aliphatic variants in series 2, proteins that eluted early in the salt gradient were not affected by the increase in ligand hydrophobicity, while the later eluting proteins bound stronger as the length of the aliphatic substituent increased. The series 3 variants indicated that phenyl ring fluorination created subtle changes in protein elution in these MM AEX systems. Retention data from the three series was used to generate a partial least squares QSAR model based on both protein and ligand descriptors which accurately predicted protein retention with a training R2 of 0.81 and a test R2 of 0.76. The retention characteristics of some prototypes such as the earlier elution and unique selectivities compared to Capto Adhere suggest that they could potentially provide unique selectivities and increased recovery for the downstream processing of both mAb and non-mAb biotherapeutics.

Protein Binding Kinetics in Multimodal Systems: Implications for Protein Separations.

In this work, quartz crystal microbalance with dissipation (QCM-D) was employed to study the kinetic processes involved in the interaction of proteins with self-assembled monolayers (SAMs) of multimodal (MM) ligands. SAMs were fabricated to mimic two chromatographic multimodal resins with varying accessibility of the aromatic moiety to provide a well-defined model system. Kinetic parameters were determined for two different proteins in the presence of the arginine and guanidine and a comparison was made with chromatographic retention data. The results indicated that the accessibility of the ligand's aromatic moiety can have an important impact on the kinetics and chromatographic retention behavior. Interestingly, arginine and guanidine had very different effects on the protein adsorption and desorption kinetics in these MM systems. For cytochrome C, arginine resulted in a significant decrease and increase in the adsorption and desorption rates, respectively, while guanidine produced a dramatic increase in the desorption rate, with minimal effect on the adsorption rate. In addition, at different concentrations of arginine, two distinct kinetic scenarios were observed. For α-chymotrypsin, the presence of 0.1 M guanidine in the aromatic exposed ligand system produced an increase in the adsorption rate and only a moderate increase in the desorption rate, which helped to explain the surprising increase in the chromatographic salt elution concentration. These results demonstrate that protein adsorption kinetics in the presence of different mobile phase modifiers and MM ligand chemistries can play an important role in contributing to selectivity in MM chromatography.

Studies on the purification of antibody fragments

Abstract Antigen-binding fragments (Fabs) are becoming increasingly prevalent as an alternative to full-length monoclonal antibodies. In this work, the digestion of a mixture of different human antibodies isotypes was optimized in terms of different parameters, including the concentration of papain and cysteine, and the digestion time. The recovery of the Fab fragments was subsequently evaluated by designing four different downstream purification schemes, where the use of affinity chromatography (protein A and L) was the most efficient to isolate the Fab fragments after IgG digestion. A rapid screening of optimal conditions for the binding of pure Fab fragments to four non-affinity chromatography resins was then performed using micro-columns fabricated in a PDMS microfluidic device. The goal of these studies was to screen and evaluate the performance of two cation exchange (carboxymethyl and heparin) and two multimodal (Capto MMC and phenyl boronate) ligands for the capture of Fabs under a wide range of pH (5–9) and conductivity (up to 8 mS/cm) conditions. Multimodal resins showed the best results in binding Fab fragments, particularly at pH 5, well below the range of isoelectric points of the target Fab molecules. In addition, these resins demonstrated to have a salt-tolerant behaviour, meaning that the binding of Fab fragments was not significantly impacted when the conductivity of the adsorption buffer was increased to near-physiological conditions (8 mS/cm).

Single Molecule Force Spectroscopy and Molecular Dynamics Simulations as a Combined Platform for Probing Protein Face-Specific Binding

Biomolecular interactions frequently occur in orientation-specific manner. For example, prior nuclear magnetic resonance spectroscopy experiments in our lab have suggested the presence of a group of strongly binding residues on a particular face of the protein ubiquitin for interactions with Capto MMC multimodal ligands ("Capto" ligands) (Srinivasan, K.; et al. Langmuir 2014, 30 (44), 13205-13216). We present a clear confirmation of those studies by performing single-molecule force spectroscopy (SMFS) measurements of unbinding complemented with molecular dynamics (MD) calculations of the adsorption free energy of ubiquitin in two distinct orientations with self-assembled monolayers (SAMs) functionalized with "Capto" ligands. These orientations were maintained in the SMFS experiments by tethering ubiquitin mutants to SAM surfaces through strategically located cysteines, thus exposing the desired faces of the protein. Analogous orientations were maintained in MD simulations using suitable constraining methods. Remarkably, despite differences between the finer details of experimental and simulation methodologies, they confirm a clear preference for the previously hypothesized binding face of ubiquitin. Furthermore, MD simulations provided significant insights into the mechanism of protein binding onto this multimodal surface. Because SMFS and MD simulations both directly probe protein-surface interactions, this work establishes a key link between experiments and simulations at molecular scale through the determination of protein face-specific binding energetics. Our approach may have direct applications in biophysical systems where face- or orientation-specific interactions are important, such as biomaterials, sensors, and biomanufacturing.

A regenerable microfluidic device with integrated valves and thin-film photodiodes for rapid optimization of chromatography conditions

The optimization of chromatography operating conditions is a lengthy and demanding task that typically requires large volumes of reagents and costly dedicated equipment. In particular, the use of multimodal chromatography, in which multiple interaction groups co-exist in the same ligand, can make the optimization process even more challenging. Nevertheless, the interest in using this emerging type of ligands has been increasing due to the enhanced selectivity and stability demonstrated by multimodal ligands in the purification of several biopharmaceuticals and their lower cost compared to biological affinity ligands. In this work, we report the development of an integrated, regenerable and portable microfluidic platform for performing a rapid screening of chromatography conditions. This platform was tested for the capture of fluorophore-labeled monoclonal antibodies directly from a cell culture supernatant using a multimodal ligand (Capto MMC). Liquid insertion in the microfluidic device was controlled by pneumatically actuated embedded valves and chromatography cycles were monitored via fluorescence measurements using thin-film a-Si:H photodiodes aligned beneath the device. The regeneration of the chromatography micro-column (70 nL) was performed in the end of each cycle, providing repeatable results over several consecutive cycles. Different buffers were successively evaluated in cycles, each cycle having duration of about 3 min, and the different adsorption and elution kinetics were compared, allowing the rapid optimization of conditions to address the capture of the monoclonal antibody from complex media. Overall, a versatile, rapid and relatively inexpensive platform to perform screening studies was developed, providing a high degree of scalability.